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Presentations

Test Endpoints

ESnet endpoints: esnet#anl-diskpt1, esnet#lbl-diskpt1, esnet#bnl-diskpt1, and esnet#cern-diskpt1; test files in /data1 directory. These are read-only endpoints with datasets varying in size and number of files; they are useful for testing network performance.
Globus test endpoints: go#ep1, go#ep2; these have a 10MB quota and are used mostly to validate that a new Globus account is working.

Exercise 1: Account Signup

  1. Go to: globus.org/signup
  2. Create your Globus account.
  3. Validate your e-mail address.
  4. Optional: Login with your campus/InCommon identity.

Exercise 2: Transfer, Sharing, Group Management

  1. Install Globus Connect Personal.
  2. Move file(s) from esnet#anl-diskpt1 to your laptop.
  3. Create a shared endpoint on your laptop.
  4. Grant your neighbor permissions on your shared endpoint.
  5. Access your neighbor’s shared endpoint.
  6. Go to globus.org/Groups and search for group named BioIT2015. Click Join the Group.

Exercise 3: Transferring data from a Sequencing center

  1. Login to bioit.globusgenomics.org.
  2. Click on Browse and Get Data using Globus Online tool on the left hand panel.
  3. Start typing the name of the endpoint: sulakhe#SequencingCenter.
  4. Log in to the endpoint with username "genomics", password "globus".
  5. Select the the forward Exome files under Exome-seq-sample data and click Execute.
  6. Repeat the above step for reverse file.

Exercise 4 : Exome Analysis Workflow

  1. Login to bioit.globusgenomics.org.
  2. Copy "dbsnp" and "1000G" files from: "Shared Data -> Data Libraries -> Reference Data Library" (into same history.)
  3. On the Main page, click on the "Workflow for Illumina Exome-Seq" and "import workflow".
  4. Run Workflow: Click Workflow tab and select the imported Exome workflow and click "Run".
  5. Input Parameters: Select appropriate input files (Forward & Reverse as well as reference files for each step.
  6. Click "Run Workflow" button.

Exercise 5

Try the Exome Workflow with Transfers jobs as inputs (Under Published Workflows).

Exercise 6: Batch submission

Useful Links

Optimizing Your Storage Systems for Data Management Services

Feel free to contact the presenters if you have questions or would like additional information:

Ravi Madduri - madduri-at-mcs-dot-anl-dot-gov
Dina Sulakhe - sulakhe-at-uchicago-dot-edu
Alex Rodriguez - arodri7-at-uchicago-dot-edu
Paul Dave - pdave-at-uchicago-dot-edu